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Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

Genome biology · 2008 · Vol. 9(1) · pp. R7–R7

Brian J. Haas✉(J. Craig Venter Institute)Steven L. Salzberg(University of Maryland, College Park)Wei Zhu(J. Craig Venter Institute)Mihaela Pertea(University of Maryland, College Park)Jonathan Allen(University of Maryland, College Park)Joshua Orvis(University of Maryland, Baltimore)Owen White(University of Maryland, Baltimore)C. Robin Buell(J. Craig Venter Institute)Jennifer R. Wortman(J. Craig Venter Institute)

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Abstract

EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.

Fractal and DNA sequence analysis Machine Learning in Bioinformatics Genomics and Phylogenetic StudiesBiologyHuman geneticsAnnotationComputational biologyGene AnnotationGeneGeneticsGenome BiologyGene predictionRNA splicing